Hironori Sato

Serum proteomics is increasingly used for minimally invasive biomarker discovery and disease phenotyping, and the choice of serum preprocessing workflow can shape proteome depth, quantitative characteristics, and downstream biological readouts. However, disease-oriented comparisons within a single cohort remain limited. Here, we compared four serum preprocessing workflows － Top14 depletion (TOP14D), tomato lectin affinity purification (TomAP), and two nanoparticle-based enrichment workflows (NPA and NPB) － using serum from six patients with systemic juvenile idiopathic arthritis (sJIA) and six age- and sex-matched healthy controls, and analyzed them using unified data-independent acquisition mass spectrometry (DIA-MS) and a statistical pipeline. We evaluated proteome depth, missingness, quantitative characteristics, group separation, differential abundance signatures, pathway enrichment, curated sJIA-related gene set coverage, pre-ranked gene set enrichment analysis (GSEA) results, and detection of inflammasome/interferon-related proteins. TomAP yielded the greatest proteome depth (7612 proteins), followed by NPB (6735 proteins) and NPA (6602 proteins), whereas TOP14D yielded the smallest protein set (3303 proteins). Principal component analysis (PCA) showed a separation between the sJIA and control groups for all workflows. Differentially expressed proteins (DEPs) showed limited overlap, with only 75 DEPs common to all four workflows. Functional enrichment patterns were workflow-dependent; TOP14D and TomAP mainly captured neutrophil/myeloid and inflammatory processes, whereas NPA and NPB captured RNA processing- and translation-related signals. TomAP showed relatively broad coverage and positive enrichment of curated sJIA-related gene sets associated with inflammation, innate immunity, and macrophage activation syndrome (MAS). Inflammasome/interferon-related proteins, including NLRC4, PYCARD, GSDMD, MEFV, IL-18, OAS3, and MYD88, showed workflow-dependent detectability and differential abundance. These findings support a disease-oriented benchmark for fit-for-purpose workflow selection according to the disease axis and analytical objective rather than proteome depth alone.

Background/Objectives: CDKL5 deficiency disorder (CDD) is a rare X-linked developmental and epileptic encephalopathy characterized by early onset refractory epilepsy and severe neurodevelopmental impairment with autistic features. Despite advances in genetic diagnosis, objective biomarkers reflecting disease mechanisms remain limited. Extracellular vesicles (EVs) circulating in the blood may contain disease-related proteins derived from the central nervous system. This study aimed to characterize the plasma EV proteome in CDD in a hypothesis-generating exploratory framework and identify the candidate molecular pathways associated with this disorder. Methods: Plasma samples from seven patients with genetically confirmed CDD and seven neurotypical developmental controls were analyzed. Extracellular vesicle-containing preparations (EVs-cp) were isolated via immunoprecipitation using antibodies against CD9, CD63, and CD81. Proteomic profiling was performed using data-independent mass spectrometry. Differentially expressed proteins were identified using Welch’s t-test with a false discovery rate correction. Functional enrichment, protein interaction network, and correlation analyses were performed using CDKL5 Clinical Severity Assessment (CCSA) scores. Results: In total, 5617 proteins were identified, of which 3510 were used for quantitative analysis. Compared to the controls, 2108 proteins were upregulated and 158 were downregulated in the CDD samples. Enrichment analysis revealed alterations in vesicle-mediated transport, cytoskeletal organization, and immune-related pathways. Several proteins were also correlated with clinical severity scores. Conclusions: Plasma EV proteomics revealed molecular alterations associated with CDD and provided a potential approach for biomarker discovery and mechanistic investigation.

Introduction: Hemophagocytic lymphohistiocytosis (HLH) is a life‐threatening hyperinflammatory syndrome caused by excessive cytokine release from activated T cells and macrophages. Primary HLH, or familial HLH (FHL), results from genetic mutations affecting cytotoxic lymphocyte function. Case Report: We present a case of FHL Type 2 (FHL2) caused by compound heterozygous variants in the PRF1 gene, including one novel missense variant of p.Ala21Val (A21V). A 5‐month‐old boy presented with persistent fever, pancytopenia, coagulopathy, hepatosplenomegaly, and elevated ferritin, meeting the HLH‐2004 diagnostic criteria. Bone marrow revealed hemophagocytosis, and NK cell activity was markedly reduced. Genetic analysis identified compound heterozygous PRF1 variants: A21V and p.Pro16Ser (P16S). Flow cytometric analysis demonstrated markedly reduced PRF1 protein expression in the patient’s NK cells. The patient was treated with etoposide, dexamethasone palmitate, and cyclosporine, followed by cord blood transplantation. The patient has been in remission for over a year. Discussion: The PRF1 A21V variant has not been described in the public database or the literature and is therefore considered a novel pathogenic variant for FHL2 with functional validation. Although the PRF1 P16S variant has been previously reported in the heterozygous state in an adult patient with primary HLH, our findings provide functional and clinical evidence supporting a contributory role of the P16S variant in autosomal recessive early‐onset FHL2 when present in trans with the novel A21V variant. Conclusion: We identified a previously unreported PRF1 variant, A21V, and provided the first functional evidence of impaired perforin expression associated with A21V/P16S, highlighting the importance of functional validation of rare PRF1 variants in FHL2.

Backgroud: Rett syndrome is a neurodevelopmental disorder that affects 1 in 10,000 females. Various treatments have been explored; however, no effective treatments have been reported to date, except for trofinetide, a synthetic analog of glycine-proline-glutamic acid, which was approved by the FDA in 2023. Serological biomarkers that correlate with the disease status of RTT are needed to promote early diagnosis and to develop novel agents. Methods: In this study, we performed a high-depth proteomic analysis of extracellular vesicles containing preparations extracted from patient plasma samples to identify novel biomarkers. Results: We identified 33 upregulated and 17 downregulated candidate proteins among a total of 4273 proteins in RTT compared to the healthy controls. Among these, UBE3B was predominantly increased in patients with Rett syndrome and exhibited a strong correlation with the clinical severity score, indicating the severity of the disease. Conclusions: We demonstrated that the proteomics of high-depth extracellular vesicles containing preparations in rare diseases could be valuable in identifying new disease biomarkers and understanding their pathophysiology.

Not-yet-known not-yet-known not-yet-known unknown Background: The innate immune system is activated at the onset of food protein-induced enterocolitis syndrome (FPIES) symptoms. However, the precise mechanism through which this immune response is initiated remains unclear. Objective: We aimed to investigate the proteomic profile of FPIES during symptom development through in-depth serum and saliva proteomic analyses. Methods: We enrolled 17 patients with a previous diagnosis of egg yolk FPIES who underwent an oral food challenge test (OFC) with 5 g of heated egg yolk. Six patients showed positive OFC results, whereas 11 showed negative OFC results. Serum and saliva samples were collected before OFC and 1 and 2 h after ingestion. Serum was also collected at symptom onset. We analyzed serum and saliva peptides using data-independent acquisition-mass spectrometry and compared levels to identify protein groups and pathways important in FPIES symptom development. Results: We detected 4,138 and 7,202 proteins in the serum and saliva, respectively. The OFC-positive group exhibited 609 serum proteins with more than a two-fold change in expression 2 h after OFC, including proteasome subunits and neddylation-related proteins. We identified 304 proteins associated with symptom onset, including those related to the degradation response and neutrophil extracellular trap formation. Proteins related to neutrophil activation increased both in the serum and saliva, regardless of the onset of symptoms. Conclusion: Our findings suggest that changes in protein levels, including proteasome and neddylation-related proteins, may be involved in FPIES pathogenesis and warrant further investigation to address the growing clinical burden imposed by gastrointestinal allergies.

Recent advances in in-depth data-independent acquisition proteomic analysis have enabled comprehensive quantitative analysis of >10,000 proteins. Herein, an integrated proteogenomic analysis for inherited bone marrow failure syndrome (IBMFS) was performed to reveal their biological features and to develop a proteomic-based diagnostic assay in the discovery cohort; dyskeratosis congenita (n = 12), Fanconi anemia (n = 11), Diamond–Blackfan anemia (DBA, n = 9), Shwachman–Diamond syndrome (SDS, n = 6), ADH5/ALDH2 deficiency (n = 4), and other IBMFS (n = 18). Unsupervised proteomic clustering identified eight independent clusters (C1–C8), with the ribosomal pathway specifically downregulated in C1 and C2, enriched for DBA and SDS, respectively. Six patients with SDS had significantly decreased SBDS protein expression, with two of these not diagnosed by DNA sequencing alone. Four patients with ADH5/ALDH2 deficiency showed significantly reduced ADH5 protein expression. To perform a large-scale rapid IBMFS screening, targeted proteomic analysis was performed on 417 samples from patients with IBMFS-related hematological disorders (n = 390) and healthy controls (n = 27). SBDS and ADH5 protein expressions were significantly reduced in SDS and ADH5/ALDH2 deficiency, respectively. The clinical application of this first integrated proteogenomic analysis would be useful for the diagnosis and screening of IBMFS, where appropriate clinical screening tests are lacking.